plot.fsa: Plot method for "fsa" objects

Description

Plots a fsa object. For each selected channel, a line is drawn bewteen measured fluorescence intensities (y axis) along the electrophoresis time (x axis).

Usage

# S3 method for fsa
plot(x, units = NA, channels = NA, chanColors = NA, ladder = TRUE,
    offScaleCol = "#FF0000", offScalePch = "+", offScaleCex = 0.4, bg = "white",
    fg = "black", title = "", title.adj = 0, title.line = NA, xlab = NA,
    ylab = "Intensity", xlim = NA, ylim = NA, xaxt = "s", yaxt = "s", bty = "o",
    xaxp = NA, nticks = 5, all.bp = TRUE, peaks.alpha = 48L, peaks.srt = 30,
    peaks.adj = c(0, 0), peaks.cex = 1.3, peaks.font = 2, legend.x = "topleft", ...)

Value

Invisibly returns TRUE on success.

Arguments

x: The fsa object to plot.
units: Single character value, the unit to use on x axis. "index" uses the raw index contained in files, "bp" usess base pair estimations but needs the object to be aligned first using align.fsa. NA will select "bp" if x is aligned, "index" elsewhere.
channels: Character or integer vector, the channels to plot. If NA, all channels are selected.
chanColors: Character vector defining colors to use to plot channels. Can be named according to channel names stored in x, or parallel with channels (first color for first channel, etc, no recycling). If NA, colors stored in x are used. See the col argument in par for further details on allowed values.
ladder: Single logical value, whether to add an x axis with size ladder peaks or not. Raises a warning if x was not aligned before plotting.
offScaleCol: To be passed to points for off-scale value plot (see par for allowed values).
offScalePch: To be passed to points for off-scale value plot (see par for allowed values).
offScaleCex: To be passed to points for off-scale value plot (see par for allowed values).
bg: See par for further details.
fg: See par for further details. This value is also used for col.axis, col.lab, col.main and col.sub graphical parameters.
title: Single character value, the main title to print on the plot.
title.adj: To be passed as adj to title.
title.line: To be passed as line to title.
xlab: See plot for further details. If NA, units is used.
ylab: See plot for further details.
xlim: See plot for further details. If NA, x range is used.
ylim: See plot for further details. If NA, x range is used.
xaxt: See par for further details.
yaxt: See par for further details.
bty: See par for further details.
xaxp: See par for further details. If NA, a suitable value is computed.
nticks: Single integer value. When xaxp is NA and units is "bp", this values fixes the interval between X axis labels.
all.bp: Single logical value, whether to force an unlabeled axis tick at each bp when units is "bp" or not.
peaks.alpha: Single integer value, the alpha channel to add to peak colors to make a background (255 is no transparency at all, 0 is invisible).
peaks.srt: To be passed as srt to text while printing peak names.
peaks.adj: To be passed as adj to text while printing peak names.
peaks.cex: To be passed as cex to text while printing peak names.
peaks.font: To be passed as font to text while printing peak names.
legend.x: To be passed as x to legend.
...: Further arguments to be passed to plot.

Author

Sylvain Mareschal

Examples

Run this code

  # Example FSA file provided
  fsa <- read.fsa(system.file("extdata/fsa_GEP/A5918.fsa", package="FSAtools"))
  
  # Plot whole profile
  plot(fsa)
  
  # Plot subset of the profile (time index)
  plot(fsa, units="index", xlim=c(4000,5000))
  
  # Plot subset of the profile (base pairs)
  fsa <- align.fsa(fsa)
  plot(fsa, units="bp", xlim=c(80,130))